Matteo Tiberti

TL;DR: PyInteraph is a software suite designed to analyze MD and structural ensembles with attention to binary interactions between residues, such as hydrogen bonds, salt bridges, and hydrophobic interactions and allows the different classes of intra- and intermolecular interactions to be represented, combined or alone, in the form of interaction graphs.

TL;DR: An easily accessible software toolkit, called ENCORE, which can be used to compare conformational ensembles generated either from simulations alone or synergistically with experiments, and demonstrates efficient computational scaling for typical analyses, and robustness against both the size and sampling of the ensemble.

TL;DR: XPyder as mentioned in this paper is an interface between one of the most employed molecular graphics systems, PyMOL, and the analysis of dynamical cross-correlation matrices (DCCM).

TL;DR: This work presents a comparative study of psychrophilic, mesophilic and thermophilic subtilisin-like serine proteases by all-atom molecular dynamics simulations in explicit solvent using a multiple-replica approach and points out a different optimization and usage of salt-bridge interactions and networks in cold- and warm-adapted enzymes.

TL;DR: It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies, and the seesaw coordination geometry of Ni was found to be a key feature for facile H2 Cleavage.